# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 07:09:55 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: ethyl 4-[(2R,4S)-2-(aminomethyl)morpholin-4-yl]-3-(3-cyanophenyl)-1H-pyrazolo[4,5-e]pyridine-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1cnc2[nH]nc(c3cccc(c3)C#N)c2c1N4CCO[C@H](CN)C4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 4YM  4YM  'ethyl 4-[(2R,4S)-2-(aminomethyl)morpholin-4-yl]-3-(3-cyanophenyl)-1H-pyrazolo[4,5-e]pyridine-5-carboxylate'  ligand  52  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4YM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 4YM  C01   C  CH3   0  -0.688   6.8404   0.3725   1.0721
 4YM  C02   C  CH2   0  -0.183   5.7991   0.8432   0.0875
 4YM  O03   O  O2    0  -0.446   4.6501  -0.0147   0.2213
 4YM  C04   C  C     0   0.520   3.6111   0.2123  -0.5622
 4YM  O05   O  O     0  -0.432   3.5531   1.1112  -1.3645
 4YM  C06   C  CR6   0  -0.170   2.5544  -0.8178  -0.3707
 4YM  C07   C  CR16  0  -0.069   2.9722  -2.1600  -0.5218
 4YM  N08   N  N     0  -0.423   2.1742  -3.2022  -0.5697
 4YM  C09   C  CR56  0   0.543   0.8938  -2.9071  -0.3779
 4YM  N10   N  NR15  0  -0.518  -0.1353  -3.7735  -0.3381
 4YM  N11   N  N     0  -0.230  -1.2838  -3.1709  -0.0342
 4YM  C12   C  CR5   0   0.186  -1.0322  -1.8909   0.1099
 4YM  C13   C  CR6   0   0.066  -2.0953  -1.0004   0.5908
 4YM  C14   C  CR16  0  -0.251  -1.8973  -0.2434   1.7457
 4YM  C15   C  CR16  0  -0.241  -2.9203   0.5323   2.2690
 4YM  C16   C  CR16  0  -0.246  -4.1548   0.5757   1.6417
 4YM  C17   C  CR6   0   0.022  -4.3533  -0.1780   0.4862
 4YM  C18   C  CSP   0   0.051  -5.6169  -0.1363  -0.1769
 4YM  N19   N  N     0  -0.248  -6.6370  -0.1035  -0.7114
 4YM  C20   C  CR16  0  -0.273  -3.3318  -0.9693  -0.0377
 4YM  C21   C  CR56  0  -0.177   0.3510  -1.6341  -0.1311
 4YM  C22   C  CR6   0   0.374   1.2018  -0.5186  -0.1935
 4YM  N23   N  N     0  -0.538   0.6417   0.7620  -0.0804
 4YM  C24   C  CH2   0  -0.329   1.2624   1.7194   0.8206
 4YM  C25   C  CH2   0  -0.198   0.3128   2.8889   0.9891
 4YM  O26   O  OC2   0  -0.482   0.0429   3.4925  -0.2552
 4YM  C27   C  CH1   0  -0.007  -0.5803   2.6180  -1.1738
 4YM  C28   C  CH2   0  -0.303  -2.0364   2.3207  -0.8317
 4YM  N29   N  NH2   0  -0.793  -2.7899   3.5356  -0.5828
 4YM  C30   C  CH2   0  -0.319   0.2419   1.3434  -1.3641
 4YM  H01   H  HCH3  0   0.242   7.7124   1.0222   1.0031
 4YM  H01A  H  HCH3  0   0.238   6.4718   0.4167   2.0968
 4YM  H01B  H  HCH3  0   0.238   7.1650  -0.6462   0.8601
 4YM  H02   H  HCH2  0   0.240   5.5052   1.8745   0.2922
 4YM  H02A  H  HCH2  0   0.241   6.1732   0.7941  -0.9368
 4YM  H07   H  HCR6  0   0.281   4.0276  -2.3668  -0.6590
 4YM  HN10  H  HNR5  0   0.425  -0.1020  -4.7753  -0.4468
 4YM  H14   H  HCR6  0   0.268  -0.9393  -0.2724   2.2475
 4YM  H15   H  HCR6  0   0.279  -2.7537   1.1093   3.1681
 4YM  H16   H  HCR6  0   0.287  -4.9546   1.1843   2.0406
 4YM  H20   H  HCR6  0   0.280  -3.5016  -1.5477  -0.9360
 4YM  H24   H  HCH2  0   0.255   1.4328   1.2441   1.7884
 4YM  H24A  H  HCH2  0   0.221   2.2224   2.1113   0.4650
 4YM  H25   H  HCH2  0   0.210  -0.6077   2.5600   1.4867
 4YM  H25A  H  HCH2  0   0.243   0.7760   3.6493   1.6197
 4YM  H27   H  HCH1  0   0.240  -0.5647   3.1511  -2.1310
 4YM  H28   H  HCH2  0   0.203  -2.4334   1.7147  -1.6593
 4YM  H28A  H  HCH2  0   0.236  -2.0909   1.6936   0.0560
 4YM  HN29  H  HNH2  0   0.338  -2.8979   4.0518  -1.4478
 4YM  HN2A  H  HNH2  0   0.343  -3.7280   3.2891  -0.2954
 4YM  H30   H  HCH2  0   0.241   1.1210   1.5739  -1.9762
 4YM  H30A  H  HCH2  0   0.252  -0.3540   0.6117  -1.9148

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 4YM  C01  C02   single    1.508  0.020  1.508
 4YM  C02  O03   single    1.440  0.020  1.440
 4YM  O03  C04   single    1.321  0.020  1.321
 4YM  C04  O05   double    1.206  0.020  1.206
 4YM  C04  C06   single    1.488  0.020  1.488
 4YM  C06  C07   aromatic  1.414  0.020  1.414
 4YM  C06  C22   aromatic  1.397  0.020  1.397
 4YM  C07  N08   aromatic  1.314  0.020  1.314
 4YM  N08  C09   aromatic  1.328  0.020  1.328
 4YM  C09  N10   aromatic  1.346  0.020  1.346
 4YM  C09  C21   aromatic  1.406  0.020  1.406
 4YM  N10  N11   aromatic  1.332  0.020  1.332
 4YM  N11  C12   aromatic  1.312  0.020  1.312
 4YM  C12  C13   single    1.468  0.020  1.468
 4YM  C12  C21   aromatic  1.427  0.020  1.427
 4YM  C13  C14   aromatic  1.395  0.020  1.395
 4YM  C13  C20   aromatic  1.387  0.020  1.387
 4YM  C14  C15   aromatic  1.386  0.020  1.386
 4YM  C15  C16   aromatic  1.385  0.020  1.385
 4YM  C16  C17   aromatic  1.394  0.020  1.394
 4YM  C17  C18   aromatic  1.428  0.020  1.428
 4YM  C17  C20   aromatic  1.394  0.020  1.394
 4YM  C18  N19   aromatic  1.152  0.020  1.152
 4YM  C21  C22   aromatic  1.404  0.020  1.404
 4YM  C22  N23   single    1.402  0.020  1.402
 4YM  N23  C24   single    1.454  0.020  1.454
 4YM  N23  C30   aromatic  1.465  0.020  1.465
 4YM  C24  C25   single    1.516  0.020  1.516
 4YM  C25  O26   aromatic  1.409  0.020  1.409
 4YM  O26  C27   aromatic  1.413  0.020  1.413
 4YM  C27  C28   single    1.525  0.020  1.525
 4YM  C27  C30   aromatic  1.529  0.020  1.529
 4YM  C28  N29   single    1.451  0.020  1.451
 4YM  C01  H01   single    0.970  0.020  1.090
 4YM  C01  H01A  aromatic  0.970  0.020  1.090
 4YM  C01  H01B  single    0.970  0.020  1.090
 4YM  C02  H02   single    0.970  0.020  1.090
 4YM  C02  H02A  single    0.970  0.020  1.090
 4YM  C07  H07   single    0.930  0.020  1.080
 4YM  N10  HN10  single    0.860  0.020  1.020
 4YM  C14  H14   single    0.930  0.020  1.080
 4YM  C15  H15   single    0.930  0.020  1.080
 4YM  C16  H16   single    0.930  0.020  1.080
 4YM  C20  H20   single    0.930  0.020  1.080
 4YM  C24  H24   single    0.970  0.020  1.090
 4YM  C24  H24A  single    0.970  0.020  1.090
 4YM  C25  H25   single    0.970  0.020  1.090
 4YM  C25  H25A  single    0.970  0.020  1.090
 4YM  C27  H27   single    0.970  0.020  1.090
 4YM  C28  H28   single    0.970  0.020  1.090
 4YM  C28  H28A  single    0.970  0.020  1.090
 4YM  N29  HN29  single    0.890  0.020  1.040
 4YM  N29  HN2A  single    0.890  0.020  1.040
 4YM  C30  H30   single    0.970  0.020  1.090
 4YM  C30  H30A  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 4YM  H01B  C01  H01A  108.75  3.000
 4YM  H01B  C01  H01   107.86  3.000
 4YM  H01A  C01  H01   107.82  3.000
 4YM  H01B  C01  C02   111.74  3.000
 4YM  H01A  C01  C02   111.56  3.000
 4YM  H01   C01  C02   108.97  3.000
 4YM  H02A  C02  H02   108.10  3.000
 4YM  H02A  C02  O03   109.49  3.000
 4YM  H02   C02  O03   109.30  3.000
 4YM  H02A  C02  C01   111.22  3.000
 4YM  H02   C02  C01   111.00  3.000
 4YM  O03   C02  C01   107.71  3.000
 4YM  C04   O03  C02   118.04  3.000
 4YM  C06   C04  O05   124.56  3.000
 4YM  C06   C04  O03   111.30  3.000
 4YM  O05   C04  O03   124.08  3.000
 4YM  C22   C06  C07   120.21  3.000
 4YM  C22   C06  C04   123.77  3.000
 4YM  C07   C06  C04   115.69  3.000
 4YM  H07   C07  N08   115.81  3.000
 4YM  H07   C07  C06   118.83  3.000
 4YM  N08   C07  C06   125.28  3.000
 4YM  C09   N08  C07   113.84  3.000
 4YM  C21   C09  N10   106.41  3.000
 4YM  C21   C09  N08   126.80  3.000
 4YM  N10   C09  N08   126.76  3.000
 4YM  HN10  N10  N11   120.17  3.000
 4YM  HN10  N10  C09   127.67  3.000
 4YM  N11   N10  C09   112.01  3.000
 4YM  C12   N11  N10   107.52  3.000
 4YM  C21   C12  C13   130.40  3.000
 4YM  C21   C12  N11   110.04  3.000
 4YM  C13   C12  N11   119.26  3.000
 4YM  C20   C13  C14   119.30  3.000
 4YM  C20   C13  C12   120.71  3.000
 4YM  C14   C13  C12   119.84  3.000
 4YM  H14   C14  C15   119.56  3.000
 4YM  H14   C14  C13   119.68  3.000
 4YM  C15   C14  C13   120.76  3.000
 4YM  H15   C15  C16   119.81  3.000
 4YM  H15   C15  C14   119.92  3.000
 4YM  C16   C15  C14   120.27  3.000
 4YM  H16   C16  C17   120.32  3.000
 4YM  H16   C16  C15   120.64  3.000
 4YM  C17   C16  C15   119.04  3.000
 4YM  C20   C17  C18   119.38  3.000
 4YM  C20   C17  C16   120.93  3.000
 4YM  C18   C17  C16   119.69  3.000
 4YM  N19   C18  C17   180.00  3.000
 4YM  H20   C20  C17   120.03  3.000
 4YM  H20   C20  C13   120.27  3.000
 4YM  C17   C20  C13   119.70  3.000
 4YM  C22   C21  C12   137.52  3.000
 4YM  C22   C21  C09   118.53  3.000
 4YM  C12   C21  C09   103.94  3.000
 4YM  N23   C22  C21   118.67  3.000
 4YM  N23   C22  C06   126.35  3.000
 4YM  C21   C22  C06   114.98  3.000
 4YM  C30   N23  C24   113.47  3.000
 4YM  C30   N23  C22   113.63  3.000
 4YM  C24   N23  C22   118.74  3.000
 4YM  H24A  C24  H24   107.85  3.000
 4YM  H24A  C24  C25   107.99  3.000
 4YM  H24   C24  C25   109.58  3.000
 4YM  H24A  C24  N23   114.10  3.000
 4YM  H24   C24  N23   109.23  3.000
 4YM  C25   C24  N23   108.03  3.000
 4YM  H25A  C25  H25   107.64  3.000
 4YM  H25A  C25  O26   107.05  3.000
 4YM  H25   C25  O26   111.61  3.000
 4YM  H25A  C25  C24   109.63  3.000
 4YM  H25   C25  C24   110.17  3.000
 4YM  O26   C25  C24   110.63  3.000
 4YM  C27   O26  C25   113.17  3.000
 4YM  H27   C27  C30   106.81  3.000
 4YM  H27   C27  C28   107.72  3.000
 4YM  C30   C27  C28   112.26  3.000
 4YM  H27   C27  O26   105.10  3.000
 4YM  C30   C27  O26   111.08  3.000
 4YM  C28   C27  O26   113.33  3.000
 4YM  H28A  C28  H28   106.16  3.000
 4YM  H28A  C28  N29   108.45  3.000
 4YM  H28   C28  N29   113.76  3.000
 4YM  H28A  C28  C27   110.07  3.000
 4YM  H28   C28  C27   106.46  3.000
 4YM  N29   C28  C27   111.78  3.000
 4YM  HN2A  N29  HN29  105.54  3.000
 4YM  HN2A  N29  C28   109.04  3.000
 4YM  HN29  N29  C28   109.61  3.000
 4YM  H30A  C30  H30   107.27  3.000
 4YM  H30A  C30  C27   109.14  3.000
 4YM  H30   C30  C27   109.00  3.000
 4YM  H30A  C30  N23   108.95  3.000
 4YM  H30   C30  N23   110.74  3.000
 4YM  C27   C30  N23   111.63  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 4YM  CONST_01  C09   N08  C07  C06     0.00   0.0  0
 4YM  CONST_02  C09   C21  C22  C06     0.00   0.0  0
 4YM  CONST_03  C12   C21  C22  C06   180.00   0.0  0
 4YM  CONST_05  C21   C22  C06  C07     0.00   0.0  0
 4YM  CONST_06  N23   C22  C06  C07   180.00   0.0  0
 4YM  CONST_07  N10   C09  N08  C07   180.00   0.0  0
 4YM  CONST_08  C21   C09  N08  C07     0.00   0.0  0
 4YM  CONST_09  C22   C06  C07  N08     0.00   0.0  0
 4YM  CONST_10  N11   N10  C09  N08   180.00   0.0  0
 4YM  CONST_11  C12   C21  C09  N08   180.00   0.0  0
 4YM  CONST_12  C22   C21  C09  N08     0.00   0.0  0
 4YM  CONST_13  C12   N11  N10  C09     0.00   0.0  0
 4YM  CONST_14  N11   C12  C21  C09     0.00   0.0  0
 4YM  CONST_15  C13   C12  C21  C09   180.00   0.0  0
 4YM  CONST_16  N23   C22  C21  C09   180.00   0.0  0
 4YM  CONST_17  C12   C21  C09  N10     0.00   0.0  0
 4YM  CONST_18  C22   C21  C09  N10   180.00   0.0  0
 4YM  CONST_19  C13   C12  N11  N10   180.00   0.0  0
 4YM  CONST_20  C21   C12  N11  N10     0.00   0.0  0
 4YM  CONST_21  C21   C09  N10  N11     0.00   0.0  0
 4YM  CONST_24  C22   C21  C12  N11   180.00   0.0  0
 4YM  CONST_25  C15   C14  C13  C12   180.00   0.0  0
 4YM  CONST_26  C17   C20  C13  C12   180.00   0.0  0
 4YM  CONST_27  N23   C22  C21  C12     0.00   0.0  0
 4YM  CONST_28  C22   C21  C12  C13     0.00   0.0  0
 4YM  CONST_29  C16   C15  C14  C13     0.00   0.0  0
 4YM  CONST_30  C16   C17  C20  C13     0.00   0.0  0
 4YM  CONST_32  C17   C20  C13  C14     0.00   0.0  0
 4YM  CONST_33  C17   C16  C15  C14     0.00   0.0  0
 4YM  CONST_34  C20   C13  C14  C15     0.00   0.0  0
 4YM  CONST_35  C20   C17  C16  C15     0.00   0.0  0
 4YM  CONST_38  C27   C30  N23  C22   180.00   0.0  0
 4YM  CONST_43  C18   C17  C20  C13   180.00   0.0  0
 4YM  CONST_44  C18   C17  C16  C15   180.00   0.0  0
 4YM  CONST_45  N08   C07  C06  C04   180.00   0.0  0
 4YM  CONST_46  C21   C22  C06  C04   180.00   0.0  0
 4YM  CONST_47  N23   C22  C06  C04     0.00   0.0  0
 4YM  CONST_48  HN10  N10  C09  N08     0.00   0.0  0
 4YM  CONST_49  H07   C07  N08  C09   180.00   0.0  0
 4YM  CONST_50  H14   C14  C13  C12     0.00   0.0  0
 4YM  CONST_51  H20   C20  C13  C12     0.00   0.0  0
 4YM  CONST_52  H15   C15  C14  C13   180.00   0.0  0
 4YM  CONST_53  H16   C16  C15  C14   180.00   0.0  0
 4YM  Var_01    C25   C24  N23  C22  -167.79  30.0  1
 4YM  Var_02    O26   C25  C24  N23   -59.18  30.0  1
 4YM  Var_03    C07   C06  C04  O03   -54.32  30.0  2
 4YM  Var_04    N29   C28  C27  O26    50.05  30.0  2
 4YM  Var_05    C06   C04  O03  C02   175.78  30.0  3
 4YM  Var_06    HN29  N29  C28  C27    69.00  30.0  3
 4YM  Var_07    H01   C01  C02  O03  -178.80  30.0  3
 4YM  Var_08    H02   C02  O03  C04    59.85  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 4YM  chir_01  C27  O26  C28  C30  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 4YM  plan-1  C12   0.020
 4YM  plan-1  C13   0.020
 4YM  plan-1  C14   0.020
 4YM  plan-1  C15   0.020
 4YM  plan-1  C16   0.020
 4YM  plan-1  C17   0.020
 4YM  plan-1  C18   0.020
 4YM  plan-1  C20   0.020
 4YM  plan-1  H14   0.020
 4YM  plan-1  H15   0.020
 4YM  plan-1  H16   0.020
 4YM  plan-1  H20   0.020
 4YM  plan-2  O03   0.020
 4YM  plan-2  C04   0.020
 4YM  plan-2  O05   0.020
 4YM  plan-2  C06   0.020
 4YM  plan-3  C04   0.020
 4YM  plan-3  C06   0.020
 4YM  plan-3  C07   0.020
 4YM  plan-3  N08   0.020
 4YM  plan-3  C09   0.020
 4YM  plan-3  N10   0.020
 4YM  plan-3  N11   0.020
 4YM  plan-3  C12   0.020
 4YM  plan-3  C13   0.020
 4YM  plan-3  C21   0.020
 4YM  plan-3  C22   0.020
 4YM  plan-3  N23   0.020
 4YM  plan-3  H07   0.020
 4YM  plan-3  HN10  0.020

